Bond Orbital Theory Research Articles

Revisiting the Case of an Intramolecular Hydrogen Bond Network Forming Four- and Five-Membered Rings in d-Glucose.

The conformational behavior of cyclic monosaccharides has been widely studied over the past years, but there is no general agreement about which effects are in fact responsible for the observed conformational preferences. A recent microwave spectroscopy study determined the conformational equilibrium of d-glucose in the gas phase with a preference for a counterclockwise arrangement of the hydroxyl groups. Nevertheless, the effects that control this orientation are still uncertain because the role of intramolecular hydrogen bonds (IHBs), electrostatic and steric repulsions is not clear. This work reports a density functional theory approach based on the conformational energies of d-glucose and of some derivatives in which the anomeric hydroxyl is replaced with hydrogen (H, small and not prone to participate in proton transfer), fluorine (F, small, electronegative, and as capable as OH of forming hydrogen bonds as a proton acceptor), and chlorine (Cl, big and not anticipated to be involved in effective hydrogen bond formation) to obtain insights into the effects of the substituent at the anomeric carbon on the arrangement of the hydroxyl groups in d-glucose. The nature of the substituents at this position is crucial to determine the orientation of the remaining hydroxyl groups. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses, in addition to NMR chemical shift calculations, have been provided to support the conformational energy outcomes. Overall, the results agree with the lack of IHBs forming four- and five-membered rings in d-glucose and emphasize that steric and electrostatic repulsions involving the hydroxyl groups in the clockwise orientation are driving forces of the conformational behavior.

Theoretical insight into the structure and bonding characteristics of Bisphenol-A. QTAIM and NBO analyses

Bisphenol-A (BPA) is considered as one of the most suspicious disruptors. Exposure to BPA may bring about possible human toxicities. BPA is an emerging contaminant widely used in manufacturing of epoxy, unsaturated polyester-styreneand polycarbonate resins. BPA is released into the environment through industrial and municipal wastewater discharges; its degradation products are probably more dangerous than BPA itself. The present study aims at a better insight into its ground state electronic and acid–base properties, and the mechanism of its thermal decomposition. Density functional theory (DFT) is utilized to study the geometry, electronic structure and electrostatic potential (ESP) for BPA. The molecule is noncoplanar with one of the phenolate moieties forced out of the plane by 57[Formula: see text]. This might very well determine the dissociation reaction pathway and in the meantime facilitates strong conjugation and considerable delocalization along the rest of the molecule. Proton affinities and deprotonation enthalpies are computed and discussed. Bonding characteristics are investigated within the natural bond-orbital (NBO) and quantum theory of atom in molecule (QTAIM) frameworks.

Theoretical evaluation of symmetrical α,α′,δ,δ′-tetramethyl cucurbit[6]uril for haloalkane 1-(3-chlorophenyl)-4-(3-chloropropyl)-piperazinium and chloroform encapsulation

In the present study, structures and electronic properties of inclusion complexes of TMeQ[6] with PZ+ and CHCl3 were investigated, using the density functional theory calculations and molecular dynamic (MD) simulations. Theoretical results at the M05-2X-D3/6-31G(d) level clearly confirm that the inclusion complex formation is energetically feasible, and PZ+@TMeQ[6] formation is more favorable than CHCl3@TMeQ[6]. Natural bond orbital and quantum theory of atoms in molecules analyses were applied to investigate the electron transfer and topological properties of the interactions of TMeQ[6] and guest compounds. Non-covalence nature, van der Waals, of the host–guest interactions was confirmed by non-covalent interactions–reduced density gradient method. Finally, the effect of solvent was taken into account by using the MD simulations. According to H-bond analysis in the MD simulations, the importance of hydrogen bonding interactions was confirmed only in PZ+@TMeQ[6] complex, the studied inclusion complexes are more stable in chloroform, because of a high value of van der Waals interactions. This study show that TMeQ[6] as a good candidate for sensing. A joint MD/QM study confirms the side chain effect of PZ+ on the response ability improvement of TMeQ[6].

Resonance bonding in XNgY (X = F, Cl, Br, I; Ng = Kr or Xe; Y = CN or NC) molecules: an NBO/NRT investigation.

Several noble-gas-containing molecules XNgY were observed experimentally. However, the bonding in such systems is still not understood. Using natural bond orbital and natural resonance theory (NBO/NRT) methods, the present work investigated bonding of the title molecules. The results show that each of the studied XNgY molecules should be better described as a resonance hybrid of ω-bonding and [Formula: see text]-type long-bonding structures: X:- Ng+ - Y, X - Ng+: Y-, and X^Y. The ω-bonding and long-bonding make competing contributions to the composite resonance hybrid due to the accurately preserved bond order conservation principle. We find that the resonance bonding is highly tunable for these noble-gas-containing molecules due to its dependence on the nature of the halogen X or the central noble-gas atoms Ng. When the molecule XNgY consists of a relatively lighter Ng atom, a relatively low-electronegative X atom, and the CN fragment rather than NC, the long-bonding structure X^Y tends to be highlighted. In contrast, the heavy Ng atom and high-electronegative X atom will enhance the ω-bonding structure. Overall, the present work provides electronic principles and chemical insights that help understand the bonding in these XNgY species.

DFT study of ortho , meta and para –pyridyl cations. Pyridynium found?

Abstract The phenyl cation has been the subject of many experimental and theoretical studies because of its importance in synthetic organic chemistry. Based on interesting experimental observations from the literature, we have computationally studied the electronic and structural effects of introducing a nitrogen atom into the aromatic ring (i.e., pyridyl rings) of phenyl cations at the M06–2X/6–311+G(d,p) level of theory. Introduction of the nitrogen at the meta and para positions destabilize the ion relative to phenyl cation by 4.61 and 5.97 kcal/mol, respectively. However, substitution at the ortho position greatly stabilizes the ion (by 16.22 kcal/mol). Analysis by Natural Bond Orbital (NBO) theory reveals that the stabilization may be traced to π -bond formation between the two adjacent atoms resulting from donation of the nitrogen lone pair to the electron-deficient carbon. The resulting ion, because of its similarity to the electronic structure of benzyne, may be considered to be a pyridynium ion. The stabilization provided by the nitrogen lone pair is also evident from analysis of the decomposition of precursor diazonium compounds where the barrier to decomposition (5.3 kcal/mol) to form the pyridynium ion is significantly lower than those leading to the unsubstituted phenyl cation and regioisomeric pyridyl cations.

Natural Bond Orbital Theory of Pseudo-Jahn-Teller Effects.

We describe a unified picture of symmetry-breaking electronic interactions that are usually described as "pseudo-Jahn-Teller (PJT) effects" and attributed to vibronic coupling but can also be associated with hyperconjugative donor-acceptor interactions in the framework of natural bond orbital (NBO) and natural resonance theory (NRT) analysis. We show how NBO/NRT descriptors offer a simplified alternative to the vibronic coupling picture of PJT effects that yields both improved cause-effect specificity and chemically enriched understanding of symmetry-breaking phenomena but with no necessary input from ground-state vibrational or excited-state electronic properties. Comparative NBO/NRT vs vibronic coupling analyses of PJT effects are illustrated for two well-known cases: trans-bending in Si2H4 and higher Group-14 homologues of ethylene and chain-kinking in cyclopentadienylideneketene (C5H4CCO) and related cumulene ketones. The conceptual and practical advantages of the NBO-based hyperconjugative approach may be expected to extend to numerous PJT-type symmetry-breaking phenomena throughout the chemical sciences.

An ab initio study of some binary complexes containing methyl fluoride and difluoromethane: red-shifting and blue-shifting hydrogen bonds

ABSTRACTThe properties of a number of hydrogen-bonded complexes of methyl fluoride and difluoromethane with a range of hydrides of the first two rows of the periodic table have been computed using ab initio molecular orbital theory. The aim of this work was to identify possible examples of blue-shifting hydrogen-bonded species analogous to those formed between fluoroform and ammonia, water, phosphine and hydrogen sulphide, reported earlier. The calculations were carried out using the Gaussian-09 program, at the second-order level of Møller–Plesset perturbation theory, and with the aug-cc-pVTZ basis sets of Dunning. The properties studied include the molecular structures, the hydrogen bond energies and the vibrational spectra. The results have been interpreted with the aid of natural bond orbital theory and the quantum theory of atoms in molecules.

Regulating Noncovalent Interactions in Amino‐Amide–Copper Complexes

The relevance of intermolecular noncovalent Cl···Cu interactions in the magnetic and biological behavior of copper complexes derived from amino amides is studied. Crystallography studies show that these complexes tend to stack, favoring noncovalent interactions (hydrogen bonding and Cu···Cl). However, the presence of substituents at the C10 and C13 positions regulates the supramolecular structures in 2. Thus, magnetic studies at 93, 293, and 353 K demonstrate that magnetic exchange is favored only by Cu–Cl···Cu interactions. Moreover, biological studies show that only those copper complexes with ferromagnetic behavior present cytotoxic activity. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) computations are used to corroborate the presence of the noncovalent interactions.

A joint QM/MD study on α-, β- and γ-cyclodextrins in selective complexation with cathinone

In this article, density functional theory (DFT) calculations and 30 ns molecular dynamic (MD) simulations were performed to investigate the ability of α-, β- and γ-cyclodextrins (CDs) to form selective complexes with cathinone. DFT calculations in the gas phase, water, chloroform and methanol reveal that the solvents, reduce the stability of the complexes. Optimized structures confirm that α-CD cannot encapsulate cathinone, completely, while other CDs showed an opposite behavior. DFT calculations indicate that cathinone has the most stable complex with γ-CD in comparison to the α- and β-CDs. Natural bond orbital and quantum theory of atoms in molecules analyses reveal that the electrostatic interactions between cathinone and CDs are the driving force of the complex formation. MD simulations confirm that different solvents play an important role in the stability of the cathinone complexes and the obtained MD results are in good agreement with the DFT calculations.

Structural and vibrational characteristics of a non-linear optical material 3-(4-nitrophenyl)-1-(pyridine-3-yl) prop-2-en-1-one probed by quantum chemical computation and spectroscopic techniques

Chalcone and its derivatives are well-known for their high non-linear optical behavior and charge transfer characteristics. The effectiveness of charge transfer via ethylenic group and increase in NLO response of the chalcone upon substitutions are of great interest. The present study focuses the structural, charge transfer and non-linear optical properties of a new chalcone derivative “3-(4-nitrophenyl)-1-(pyridine-3-yl) prop-2-en-1-one” (hereafter abbreviated as 4 NP3AP). To accomplish this task, we have incorporated the experimental FT-IR, FT-Raman and UV–vis spectroscopic studies along with quantum chemical calculations. The frequency assignments of peaks in IR and Raman have been done on the basis of potential energy distribution and the results were compared with the earlier reports on similar kind of molecules. For obtaining the electronic transition details of 4 NP3AP, UV–vis spectrum has been simulated by considering both gaseous and solvent phase using time-dependent density functional theory (TD-DFT). The HOMO-LUMO energy gap, most important factor to be considered for studying charge transfer properties of the molecule has been calculated. The electron density surface map corresponding to the net electrostatic point charges has been generated to obtain the electrophilic and nucleophilic sites. The charge transfer originating from the occupied (donor) and unoccupied (acceptor) molecular orbitals have been analyzed with the help of natural bond orbital theory. Moreover, the estimation of second-hyperpolarizability of the molecule confirms the non-linear optical behavior of the molecule.

Interactions of Deferasirox as a Chelating Agent with Al and Ga Cations: A Theoretical Study on the [M(DFX)2]3- Nanostructures

A theoretical study was performed to evaluate the defersirox potency to chelate aluminum (Al) and gallium (Ga) as the toxic metals in biological systems. Deferasirox as an important class of chelators, which binds to the metallic center with the ratio of 1:2, is used to remove the toxic metals in the case of iron overload disease. The effects of water and DMSO as the solvent on the electronic nanostructures of [Al(DFX)2]3- and [Ga(DFX)2]3- were investigated by using the density functional theory and compared with the gas phase results. Natural bond orbital and quantum theory of atoms in molecules analyses was carried out to understand the nature of the complex bond character in the complexes. Topological analysis verified that deferasirox –aluminum complex is more stable than gallium complex, which is in good agreement with the experimental data. Natural charge analysis revealed that aluminum has a more positive character in comparison to gallium, therefore electron-donor atoms of the deferasirox bind to aluminum more favorable than gallium. TD-DFT studies showed a blue shift in the absorption spectra for the complexes in the presence of solvent. Based on different analyses, deferasirox is considered as a good chelator to remove aluminum and gallium cations in the biological systems.

Molecular structure, spectroscopic studies, and copper[sbnd]oxygen bond strength of α-methyl and α-ethyl derivatives of copper (II) acetylacetonate; Experimental and theoretical approach

This paper presents a combined experimental and theoretical study on the CuO bond strength of copper (II) α-methylacetylacetonate, Cu(3-Meacac)2, and copper (II) α-ethylacetylacetonate, Cu(3-Etacac)2, complexes in comparison to that in copper (II) acetylacetonate, Cu(acac)2. For this purpose, the molecular structure, UV spectra, and complete vibrational assignment of target molecules were investigated by DFT, Natural Bond Orbital (NBO) theory, and Atoms-in-Molecules (AIM) analysis at the B3LYP/6-311G* level of theory. The mentioned results are compared with those in Cu(acac)2. Fourier transform-Raman, IR, and UV spectra of these complexes have been also recorded. A complete assignment of the observed band frequencies has been done. All theoretical and experimental spectroscopic results are consisting with a stronger metal-oxygen bond in Cu(3-Meacac)2 and Cu(3-Etacac)2 complexes compared with Cu(acac)2. In addition, these results confirm that there is no significant difference between the CuO bond strength of the Cu(3-Meacac)2 and Cu(3-Etacac)2 complexes.

Naringenin encapsulation in β-CD and in heptakis(2,6-di-O-methyl)-β-CD:NMR, NBO and QTAIM analysis

Using quantum chemistry, we modeled the docking process of flavanone Naringenin guest molecule (Narg) in the host β-Cyclodextrin (β-CD) and also in modified heptakis(2,6-di-O-methyl)-β-CD (DIMEB). The effect of host methylation on the complexation behavior was highlighted through structural, electronic and nuclear studies. All ONIOM2 combinations of PM3 with B3LYP, M06-2X and wB97X-D methods at 6-31G (d) basis set, agree on the inclusion mode and the optimum 3D structure. We found a deep insertion of the hydroxy phenyl ring in the hydrophobic cavity of both hosts. On the other hand, only a partial inclusion of the hydroxy chromanone moiety, located nearby the primary rim in Narg/DIMEB complex 1 and the secondary rim in Narg/DIMEB complex 2 was found. Ground state calculations show that complex 1 is more stable than complex 2, which corroborates well with experimental results. We investigated Frontier Molecular Orbitals and global reactivity descriptors and we identified the interaction sites, the nature and the strength of intermolecular interactions using 1H NMR GIAO (Gauge-Including Atomic Orbital) method, Natural Bond Orbital (NBO) and Quantum Theory of Atom In Molecule (QTAIM) analysis. Particularly, the multifaceted nature of H-bonding interaction has been explained with QTAIM topological model which revealed the stabilization via the closed-shell interactions: C–H…H and O–H…O for both complexes, O–H…H and C–H…C for Narg/β-CD and Narg/DIMEB, respectively. QTAIM topological properties correlate well with the structural geometry and interactions predicted by both GIAO NMR and NBO analysis.

The influence of the negative hyperconjugation is relevant for the analysis of the π-π* conjugation with the mono-substitution and di-substitution of H2C= by O= and/or HN= in trans-buta-1,3-diene?

We have studied prop-2-en-1-imine (1), prop-2-enal (2), ethane-1,2-diimine (3), ethanedial (4), and 2-iminoacetaldehyde (5) to investigate the influence of the negative hyperconjugation in π-π* interaction with the substitution of =CH2 by =NH and/or =O in trans-buta-1,3-diene (6). The analyzes of the π-π* interaction performed from evaluation of the π molecular orbital diagrams and electron localization function method demonstrated, that compared to 6, the substituted compounds 1-5 presented lower electron conjugation, especially in the structures bearing =O. The geometric parameters, natural bond orders, and topological analysis realized by quantum theory of atoms in molecules method indicated a predominant C-C and C=C character for the simple and double C-C bonds in the substituted compounds, 1-5, as compared to 6. Compound 4 had the highest enthalpy of formation, which reflected the lowest π-π* interaction, maintained by the two =O conjugated groups. The natural bond orbital (NBO) and natural resonance theory (NRT) methods revealed that the π-π* electron delocalization in substituted compounds, 1-5, is lower than in 6 from, firstly, of the less favorable interactions: π(X=C) ➔ π*(C=C) and π(X=C) ➔ π*(C=X), despite of the larger π(C=C) ➔ π*(C=X) conjugation, with X = N and/or O, of 1-5 than π(C=C) ➔ π*(C=C) of 6. But, most importantly, the weight of the interaction: nπ(O) ➔ σ*(C-C), was determined from NBO and NRT methods as proportional to the π-π* conjugation and thus demonstrating be decisive to establish the level of π electronic delocalization.

Band offsets in new BN/BX (X = P, As, Sb) lateral heterostructures based on bond-orbital theory

Identifying heterostructures with tunable band alignments remains a difficult challenge. Here, based on bond-orbital theory, we propose a series of new BN/BX (X = P, As, Sb) lateral heterostructures (LHS). Our first principles calculations reveal that the LHS interlines have a substantial impact on the electronic properties. Importantly, we start with the chemical concepts, such as bond length and strength as well as orbital overlap interaction, in an attempt to thoroughly investigate the electronic properties, namely the band offset, the band gap (Eg) and the state of the energy level. We demonstrate that the newly designed BN/BX LHS have profound implications for developing advanced optoelectronics, such as high-performance light-emitting diodes and lasers. Furthermore, the new BN/BX LHS designed from the chemical viewpoint can shed new light on overcoming the enormous hurdle of ineffective and laborious material design.

Thermodynamic and kinetic analysis of the reaction between biological catecholamines and chlorinated methylperoxy radicals

ABSTRACTThe antiradical potency of catecholamines (dopamine, epinephrine, norepinephrine, L-DOPA), metabolites of dopamine (homovanillic acid, 3-methoxytyramine and 3,4-dihydroxyphenylacetic acid) and catechol towards substituted methylperoxy radicals is investigated. The thermodynamic parameters, together with the kinetic approach, are used to determine the most probable mechanism of action. The natural bond orbital and quantum theory of atoms in molecules are utilised to explain the highest reactivity of trichloromethylperoxy radical. The preferred mechanism is dependent both on the thermodynamic and kinetic parameters . The number of chlorine atoms on radical, the presence of intra-molecular hydrogen bond and number of hydroxy groups attached to the aromatic ring significantly influence the mechanism. The results suggest that sequential proton loss electron transfer (SPLET) is the most probable for reaction with methylperoxy and hydrogen atom transfer (HAT) for reaction with trichloromethylperoxy radicals, with a gradual transition between SPLET and HAT for other two radicals. Due to the significant deprotonation of molecules containing the carboxyl group, the respective anions are also investigated. The HAT and SPLET mechanisms are highly competitive in reaction with MP radical, while the dominant mechanism towards chlorinated radicals is HAT. The reactions in methanol and benzene are also discussed.

Arrangement and nature of intermolecular hydrogen bonding in complex biomolecular systems: modeling the vitamin C---L-alanine interaction

Vitamin C is known as an essential dietary supplement and implicated in diverse biological processes. We present here a theoretical study on the nature of hydrogen bonding of vitamin C in biological systems. For this reason, the complexes of vitamin C (VC) with neutral and zwitterionic L-alanine (as the simplest chiral amino acid) were studied at the MP2/6-311++G(d,p) level of theory. In the gas phase, neutral L-alanine leads to more stable complexes than the zwitterionic forms while the reverse is true in the aqueous phase. The complexes are formed via two hydrogen bond interactions, which result in a ring-like hydrogen-bonded networks. The nature of H-bonds was characterized in terms of natural bond orbital and quantum theory of atoms in molecule analyses (QTAIM). The H-bonds in the studied complexes were electrostatic in nature; however, in the case of shorter and directional H-bonds and ionic interactions, contributions of covalent character were also non-negligible. Natural energy decomposition analysis of hydrogen-bonded complexes reveals that the charge transfer and electrical components are the largest contributors for the interaction energies of complexes. Natural resonance theory analysis suggests higher resonance weight for charge-assisted interactions of vitamin C---alanine (zwitterionic) complexes, where the total interaction energy is considerably higher than that of neutral alanine.

Selective Binding of Cyclic Nanopeptide with Halides and Ion Pairs; a DFT-D3 Study

In this article, theoretical studies on the selective complexation of the halide ions (F¯, Cl¯ and Br¯) and ion pairs (Na+F¯, Na+Cl¯ and Na+Br¯) with the cyclic nano-hexapeptide (CP) composed of L-proline have been performed in the gas phase. In order to calculate the dispersion interaction energies of the CP and ions, DFT-D3 calculations at the M05-2X-D3/6-31G(d) level was employed. Based on the results, F¯ and Na+F‌¯ make the most stable complex with the CP. The dispersion interactions between the ions and the CP are small while the electrostatic interactions are the driving force of the complex formation. Finally, natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses indicate that F¯ makes the most stable complex with CP due to more charge transfer and stronger bond formation in comparison to other ions.

Geometric and Electronic Structures of Vanadium Sub-nano Clusters, Vn (n = 2-5), and their Adsorption Complexes with CO and O2 Ligands: A DFT-NBO Study

In this study, electronic structures of ground state of pure vanadium sub-nano clusters, Vn (n=2-5), and their interactions with small ligands for example CO and triplet O2 molecules are investigated by using density functional theory (DFT) calibration at the mPWPW91/QZVP level of theory. The favorable orientations of these ligands in interaction with pure vanadium sub-nano clusters were determined. Multiplicities of these pure clusters are triple, doublet, singlet and doublet for dimer, trimer, tetramer and pentamer, respectively. While the CO molecule is associatively adsorbed on vanadium clusters, triplet O2 is dissociated over adsorption. Primary and secondary hyper-conjugation concepts have been employed to show stabilization of vanadium oxide complexes. Natural bond orbital (NBO) and natural resonance theory (NRT) analysis revealed that trimer, tetramer and pentamer clusters are relatively delocalized and have some resonance structures.

Long-Bonding in HNgCN/NC (Ng = Noble Gas) Molecules: An NBO/NRT Investigation.

Recently, Weinhold et al. put forward one new concept of σ̂-type long-bonding and applied it to the comprehension of halogen noble-gas hydrides HNgY (Ng = noble gas; Y = halogen) bonding. The present study extends this new concept into HNgX (X = CN, NC) pseudohalogen molecules. At the B3LYP and CCSD(T) levels of theory, we perform natural bond orbital (NBO) and natural resonance theory (NRT) studies on the HNgX molecules and compare them with the previous results for HNgY molecules. The NBO/NRT results clearly reveal that each of the HNgX, but not the HHeCN, HNeCN, and HNeNC molecules, is composed of three leading resonance structures: two ω-bonding structures H-Ng+:X-, H:-Ng+-X and one long-bonded structure H∧X. This result indicates that the conventional long-bonding exists in these pseudohalogen molecules, like the long-bonding in HNgY molecules. Unexpectedly, we identify a new type of longer long-bonded structure H∧C in HNeNC molecule at the B3LYP level, which disappears at the CCSD level. This misleading prediction at the B3LYP level can be traced back to the singlet diradical character, which induces a low-quality geometry. Therefore, the geometry reoptimization of the noble-gas hydrides is indispensable using CASSCF-based methods, if the noble-gas hydrides fail the "Stable" test because of diradical-type instability.